Bioperl: A greedy consensus builder

[Ruediger Hornig]

Mike Cariaso (mcariaso@genelogic.com) wrote:

> To scratch an itch I've built a small object which ISA
> Bio::UnivAln.
> It has a single method 'greedy' which constucts a consensus
> sequence using a
> somewhat different method. The approach does ignores alignment
> gaps that are
> before (or after) the first (last) non-gap of a row. An example
> may explain it
> more clearly.

While we are at collecting methods for the alignment object...

I have written something which may be useful for working with
protein sequence alignments. The UnivAln->consensus method
returns identity, while I was interested in homology (eg.
V|I|A|L). So if identity of a column does not make the threshold,
but the residues with a certain property do, the property will be
returned. 

VSPEF
ASPEF
ISPDF
LTPDF

!SP~F is the 0.75 consensus with ! aliphatic and ~ acidic. If
someone is interested in this type of consensus, or in separate 
identity and homology methods in that
context, I'm happy to contribute that.

Rüdi

-- 
Dr Rüdiger Hornig
Computational Molecular Biology And Drug Design
Department For Biochemistry And Molecular Biology
Australian National University, Canberra 0200, Australia
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